[med-svn] [Git][med-team/htslib][master] 7 commits: d/watch: version=5
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 16 12:39:10 BST 2026
Andreas Tille pushed to branch master at Debian Med / htslib
Commits:
42c97142 by Andreas Tille at 2026-09-16T11:25:10+02:00
d/watch: version=5
- - - - -
bc511f18 by Andreas Tille at 2026-09-16T13:32:32+02:00
d/copyright: review; Add d/lrc.config
- - - - -
e35f6c2d by Andreas Tille at 2026-09-16T12:32:45+01:00
debian/copyright: use spaces rather than tabs to start continuation lines.
Changes-By: lintian-brush
Fixes: lintian: source: tab-in-license-text debian/copyright:8
Fixes: lintian: source: tab-in-license-text debian/copyright:9
See-also: https://lintian.debian.org/tags/tab-in-license-text.html
- - - - -
8d23cb70 by Andreas Tille at 2026-09-16T12:32:46+01:00
Remove redundant Priority: optional from source stanza.
Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html
- - - - -
9ce5e49e by Andreas Tille at 2026-09-16T12:32:47+01:00
Update standards version to 4.7.4, no changes needed.
Upgrade checklist verified:
4.7.3 → 4.7.4:
* Package is not in non-free-firmware
Changes-By: lintian-brush
Fixes: lintian: source: out-of-date-standards-version 4.7.2 (released 2025-02-27) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html
- - - - -
3b789c47 by Andreas Tille at 2026-09-16T13:33:54+02:00
Update changelog
- - - - -
c6873bf2 by Andreas Tille at 2026-09-16T13:34:17+02:00
cme fix dpkg-control
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+htslib (1.22.1+ds2-2) UNRELEASED; urgency=medium
+
+ * d/watch: version=5
+ * d/copyright: review
+ * Add d/lrc.config
+ * debian/copyright: use spaces rather than tabs to start continuation lines.
+ * Remove redundant Priority: optional from source stanza.
+ * Update standards version to 4.7.4, no changes needed.
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Sep 2026 13:33:44 +0200
+
htslib (1.22.1+ds2-1) unstable; urgency=medium
* Properly clean the upstream release tarball.
=====================================
debian/control
=====================================
@@ -1,22 +1,23 @@
Source: htslib
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>,
- Michael R. Crusoe <crusoe at debian.org>,
- Steffen Moeller <moeller at debian.org>,
- Étienne Mollier <emollier at debian.org>
+Uploaders:
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Michael R. Crusoe <crusoe at debian.org>,
+ Steffen Moeller <moeller at debian.org>,
+ Étienne Mollier <emollier at debian.org>,
Section: science
-Priority: optional
-Build-Depends: dpkg-dev (>= 1.22.5),
- debhelper-compat (= 13),
- libbz2-dev,
- libcurl4-gnutls-dev,
- liblzma-dev,
- libssl-dev,
- zlib1g-dev,
- libdeflate-dev,
- libhtscodecs-dev
-Standards-Version: 4.7.2
+Build-Depends:
+ dpkg-dev (>= 1.22.5),
+ debhelper-compat (= 14),
+ libbz2-dev,
+ libcurl4-gnutls-dev,
+ liblzma-dev,
+ libssl-dev,
+ zlib1g-dev,
+ libdeflate-dev,
+ libhtscodecs-dev,
Vcs-Browser: https://salsa.debian.org/med-team/htslib
Vcs-Git: https://salsa.debian.org/med-team/htslib.git
Homepage: https://github.com/samtools/htslib
@@ -26,14 +27,19 @@ Package: libhts3t64
Architecture: any
Multi-Arch: same
Section: libs
-Depends: ${misc:Depends},
- ${shlibs:Depends}
-Pre-Depends: ${misc:Pre-Depends}
-Breaks: libhts3 (<< ${source:Version}),
- libtabixpp (<< 1.0.0-5~),
- samtools (<< 1.17~)
-Provides: ${t64:Provides}
-Replaces: libhts3
+Depends:
+ ${misc:Depends},
+ ${shlibs:Depends},
+Pre-Depends:
+ ${misc:Pre-Depends},
+Breaks:
+ libhts3 (<< ${source:Version}),
+ libtabixpp (<< 1.0.0-5~),
+ samtools (<< 1.17~),
+Provides:
+ ${t64:Provides},
+Replaces:
+ libhts3,
Description: C library for high-throughput sequencing data formats
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
@@ -49,13 +55,14 @@ Package: libhts-dev
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libbz2-dev,
- libhts3t64 (= ${binary:Version}),
- libcurl4-gnutls-dev,
- libdeflate-dev,
- liblzma-dev,
- zlib1g-dev,
- ${misc:Depends}
+Depends:
+ libbz2-dev,
+ libhts3t64 (= ${binary:Version}),
+ libcurl4-gnutls-dev,
+ libdeflate-dev,
+ liblzma-dev,
+ zlib1g-dev,
+ ${misc:Depends},
Description: development files for the HTSlib
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
@@ -76,8 +83,9 @@ Description: development files for the HTSlib
Package: htslib-test
Architecture: all
Multi-Arch: foreign
-Depends: ${misc:Depends},
- ${perl:Depends}
+Depends:
+ ${misc:Depends},
+ ${perl:Depends},
Description: Test data for HTSlib
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
@@ -93,8 +101,9 @@ Description: Test data for HTSlib
Package: tabix
Architecture: any
-Depends: ${misc:Depends},
- ${shlibs:Depends}
+Depends:
+ ${misc:Depends},
+ ${shlibs:Depends},
Description: generic indexer for TAB-delimited genome position files
Tabix indexes files where some columns indicate sequence coordinates: name
(usually a chromosome), start and stop. The input data file must be position
=====================================
debian/copyright
=====================================
@@ -5,8 +5,8 @@ Source: https://github.com/samtools/htslib/releases
Files-Excluded: htscodecs
config.h.in
configure
- config.guess
- config.sub
+ config.guess
+ config.sub
Files: *
Copyright: © 2012-2024 Genome Research Ltd.
@@ -15,80 +15,20 @@ Copyright: © 2012-2024 Genome Research Ltd.
© 2008-2012 by Attractive Chaos <attractor at live.co.uk>
License: MIT
+Files: header.*
+Copyright: 2018-2020, 2023, 2025 Genome Research Ltd.
+ James Bonfield <jkb at sanger.ac.uk>, Valeriu Ohan <vo2 at sanger.ac.uk>
+License: BSD-3-Clause
+
Files: cram/*
Copyright: © 2012-2014 Genome Research Ltd.
© 1995-2003 MEDICAL RESEARCH COUNCIL
-License: Various_BSD-3-Clause
- The files in the 'cram' directory are under one or both of the following
- licenses.
- .
- ---------------------------------------------------------------------------
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
- 1. Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- .
- 2. Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- .
- 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
- Institute nor the names of its contributors may be used to endorse or promote
- products derived from this software without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- .
- ---------------------------------------------------------------------------
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
- 1 Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- .
- 2 Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- .
- 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
- MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
- promote products derived from this software without specific prior written
- permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License: BSD-3-Clause
Files: md5.c
-Copyright: No copyright is claimed
-License: solar-MD5
- This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
- MD5 Message-Digest Algorithm (RFC 1321).
- .
- Homepage:
- http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
- .
- Author:
- Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
- .
+Copyright: Copyright (c) 2001 Alexander Peslyak
+ James Bonfield <jkb at sanger.ac.uk>
+License: public-domain
This software was written by Alexander Peslyak in 2001. No copyright is
claimed, and the software is hereby placed in the public domain.
In case this attempt to disclaim copyright and place the software in the
@@ -121,3 +61,30 @@ License: MIT
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ Institute nor the names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,4 @@
+m4/hts_check_compile_flags_needed.m4
+m4/hts_prog_cc_warnings.m4
+LICENSE
+hts_time_funcs.h
=====================================
debian/watch
=====================================
@@ -1,3 +1,7 @@
-version=4
-opts="repack,repacksuffix=+ds,dversionmangle=auto,compression=bz2,uversionmangle=s/-rc/~rc/" \
- https://github.com/samtools/htslib/releases .*/htslib-(\d\S*)\.tar\.bz2
+Version: 5
+
+Template: Github
+Dist: https://github.com/samtools/htslib
+Dversion-Mangle: auto
+Repack-Suffix: +ds
+Uversion-Mangle: s/-rc/~rc/
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/38e6db214776d68098f4fc0b79f09fad0dbd7ac9...c6873bf28ebbe6977e9b22390bd6f919c496182f
--
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/38e6db214776d68098f4fc0b79f09fad0dbd7ac9...c6873bf28ebbe6977e9b22390bd6f919c496182f
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